We can now confirm that Atlus’ parent company, Index Holdings has been bought out by SEGA Sammy for ¥14 billion, or around $141.6 million USD. The news was confirmed by Atlus itself, via their official Twitter feed: https://twitter.com/atlus_jp/status/380274765572751360
Information is still breaking on the deal, but the Atlus brand will officially join SEGA on November 1st. This news seems to make the most sense as it will allow Atlus to remain a third party publisher. Prior rumors had pegged Nintendo and Sony as potential buyers, but it was SEGA Sammy that eventually won out in the end.
I expect more detailed information to break in the coming hours, so I’ll likely have an update from Atlus itself shortly.
Update: SEGA Sammy will acquire Index Holdings, and form a new subsidiary called SEGA Dream Corporation, albeit this name is open to change. There has been no mention if the Atlus brand will be discontinued or not.